Lightnews — Scholar-powered news

Reposted by Nick Loman

Robert Aboukhalil @robert.bio · 21h

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Stephen Turner @stephenturner.us · 20h

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪
MetaGraph: metagraph.ethz.ch
Code: github.com/ratschlab/me...

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Reposted by Nick Loman

UK Health Security Agency @ukhsa.bsky.social · 22h

#UKHSAVirusWatch is back, a summary of our weekly winter surveillance report .🦠🧵
This week's data shows an increase in COVID-19 activity, which is circulating at medium levels. Flu activity has also increased, particularly in those aged 15 to 24, but remains at baseline levels.

Graph showing COVID-19 positive tests rising steadily from spring 2025 after a low in early 2025. Data from October 2024 to October 2025, England only.

Graph showing flu-positive tests peaking sharply in winter 2024–25 before declining and then beginning to rise again in autumn 2025. Data from October 2024 to October 2025, England only.

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Nick Loman @pathogenomenick.bsky.social · 1d

Keeping phone off secret to winning Nobel

Nicholas Whyte @nwhyte.bsky.social · 1d

Dr Ramsdell, whose phone had been on airplane mode, told the BBC's Newshour Programme that his first response when his wife said, "You've won the Nobel prize" was: "I did not."

To which Ms O'Neill replied that she had 200 text messages that suggested he had.

www.bbc.com/news/article...

Scientist on three-week off-grid hike finds out he's won the Nobel prize

Dr Fred Ramsdell was "living his best life" offline when the Nobel committee tried to contact him.

www.bbc.com

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Josie Bryant @josiebryant.bsky.social · 1d

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.

🚨 Submit your abstracts now! 🚨

Please RT

coursesandconferences.wellcomeconnectingscience.org/event/air-20...

AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211

Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.

coursesandconferences.wellcomeconnectingscience.org

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Nick Loman @pathogenomenick.bsky.social · 2d

Love this!

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Reposted by Nick Loman

Alan McNally @alanmcn1.bsky.social · 3d

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest

microbiologysociety.org

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Esther Schindler @estherschindler.bsky.social · 3d

I just saw someone use the abbreviation “AI;DR” and I’ll be laughing for a while.

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Adam Rawnsley @arawnsley.bsky.social · 6d

Was curious about JFK’s health so I asked google. TIL he was pregnant in 1960 but only put on 15-20lbs

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Sathnam Sanghera @sathnam.bsky.social · 7d

Please let this be true.

Have we passed peak social media? - on.ft.com/4pTb1Di via @FT

Have we passed peak social media?

As platforms degrade into outrage and slop, users are turning away

on.ft.com

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Dan Portik @dportik.bsky.social · 8d

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

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Reposted by Nick Loman

Stephen Curry @scurry.bsky.social · 10d

As the @royalsociety.org council meets on 01 Oct to discuss the repudiation of its core values by one of its fellows, Elon Musk, I respectfully remind them of my proposals for actions that should help the RS recover its standing in the scientific community. occamstypewriter.org/scurry/2025/...

Conduct Unbecoming – how can the Royal Society escape its Musk box? | Reciprocal Space

occamstypewriter.org

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Larry Hunter @proflhunter.bsky.social · 10d

As a survivor of the last AI winter, I endorse Cory's take: "Plan for a future where you can buy GPUs for ten cents on the dollar...[and] there's a ton of extremely promising open source models that have barely been optimized and have vast potential for improvement." pluralistic.net/2025/09/27/e...

Pluralistic: The real (economic) AI apocalypse is nigh (27 Sep 2025) – Pluralistic: Daily links from Cory Doctorow

pluralistic.net

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Tami Lieberman @contaminatedsci.bsky.social · 10d

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

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Phase Genomics @phasegenomics.bsky.social · 10d

In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com

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Joseph Cherabie MD MSc (They/He) @jncherabiemd.bsky.social · 10d

And the CDC has officially decided to switch back from Mpox to Monkeypox. A reminder, the world still uses Mpox, this disease does not come from monkeys, Mpox is less stigmatizing and racist. Switching back is just meaningless, unnecessary, racist, and homophobic.

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Katie Martin @katie0martin.ft.com · 12d

We worry about Very Online Kids much more than their Very Online Parents, and I'm not sure that's wise

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Deena Mousa @deenamousa.com · 15d

In 2016 Geoffrey Hinton said “we should stop training radiologists now" since AI would soon be better at their jobs.

He was right: models have outperformed radiologists on benchmarks for ~a decade.

Yet radiology jobs are at record highs, with an average salary of $520k.

Why?

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Jeffrey Barrett @jeffbarrett.eu · 15d

The science is, in fact, clear. Good studies [1] consistently show a weak association between tylenol & autism. Those studies are very careful to say they can't establish whether this is causal. A huge Swedish study used a clever sibling design to address this, and showed zero causal effect [2].

NPR @npr.org · 16d

The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.

When it comes to Tylenol, what are parents to do?

The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.

n.pr

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Susan Kaye Quinn is Writing Solarpunk 🌞🌱 @susankayequinn.bsky.social · 15d

They've lost the 9yos

JA Westenberg
@Daojoan@mastodon.social

My 9 year old and his classmates have started using “that’s AI” to mean “I don’t believe you.”

Me: we’re having dinosaur meat for dinner

Kiddo: that’s AI
Sep 24, 2025, 07:36 AM

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Nick Loman @pathogenomenick.bsky.social · 15d

How many shopping days til Xmas

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Anna Cusco @annacusco.bsky.social · 17d

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

www.biorxiv.org

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Joshua Weitz @joshuasweitz.bsky.social · 17d

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.

jamanetwork.com/journals/jam...

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

jamanetwork.com

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Nick Loman @pathogenomenick.bsky.social · 17d

The scariest bit was when Chris cycled through London with his kids

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Greg Fell @felly500.bsky.social · 17d

www.sciencemediacentre.org/expert-react...

Hard to know what to say really
Fortunately Sci Media Centre is on hand....

@sciencemediacentre.bsky.social

expert reaction to media reports that the Trump administration will link paracetamol to autism | Science Media Centre

www.sciencemediacentre.org

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